WWW service:Pol3scan - recognition of Pol III intragenic control regions

Riccardo Percudani riccardo at irisbioc.bio.unipr.it
Thu Sep 7 11:06:56 EST 1995


[ Article crossposted from bionet.software ]
[ Author was Riccardo Percudani ]
[ Posted on 6 Sep 1995 17:49:09 GMT ]



Pol3scan recognizes the eukaryotic internal control regions A box and 
B box that are typical of tRNA genes and tDNA-derived elements.

	The program is available through WWW:
	http://irisbioc.bio.unipr.it/pol3scan.html

The algorithm is based on the statistical analysis of a database of
231 tRNA promoter regions and makes use of weight matrices and weight
vectors for scoring. The program discriminates between tRNA genes and 
related class III elements (e.g. tDNA-derived SINEs) on the basis of 
the presence of a transcriptional terminator signal and of the 
base-pairing within the aminoacyl stem.

The accuracy of the prediction was estimated by scanning the eukaryotic 
nuclear sequences present in the rel. 33 of the EMBL database (65180 entries).
The program correctly identified 932 of 940 known tRNA genes (0.85% of
false negatives) with a false positive rate of 0.0018%.



Reference:

Pavesi A., Conterio F., Bolchi A., Dieci G., and Ottonello S.(1994). 
Identification of new eucariotic tRNA genes in genomic databases by a 
multistep weight matrix analysis of transcriptional control regions, 
Nucleic Acids Res. 22, 1247-1256.




Comments about, suggestions about or corrections are welcomed.
Regards,

Riccardo Percudani
Institute of Biochemical Sciences
University of Parma                   Phone:   (+39)-521-905-646
Viale delle Scienze                     Fax:   (+39)-521-905-151
43100 Parma, Italy                   E-mail: riccardo at irisbioc.bio.unipr.it










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